Hi all,
I am trying to backmap some atomistic lipids ( CHARMM36 ) to CG like POPC
using backward.py. I am just wondering it creates 13 CG lipids (below)
which match the old martini lipid itp file
1POPC NC3 1 0.240 -0.203 1.929
1POPC PO4 2 0.051 -0.284 1.824
1POPC GL1 3 -0.199 -0.211 1.765
1POPC GL2 4 -0.025 -0.035 1.685
1POPC C1A 5 0.116 -0.225 1.328
1POPC C2A 6 0.243 -0.190 0.882
1POPC C3A 7 0.155 -0.049 0.615
1POPC C4A 8 0.037 -0.006 0.356
1POPC C1B 9 -0.288 -0.416 1.460
1POPC C2B 10 -0.158 -0.622 1.286
1POPC D3B 11 -0.231 -0.559 0.992
1POPC C4B 12 -0.187 -0.462 0.639
1POPC C5B 13 -0.204 -0.485 0.356
But the new martini_lipid itp file contains 12 CG lipids. Insane.py create
12 CG lipids for POPC and also for POPG.
In this situation, I have tried both ways to get the area per lipid at
surface tension 0 mN/m and 20 mN/m of 1024 DPPC+POPC lipids (512 lipids
each layer). I have used nearly 14000 CG water between two lipids
monolayers. The area per lipid I got is 0.5593nm2 and 0.5978nm2 for 0 and
20mN/m surface tension respectively. Temperature for both cases is 310K. As
far I know at 0 surface tension the area per lipid must be lower than
0.50nm2.
How can I address this problem?
N.B. I got the area per lipid nearly 0.474 nm2 and 0.584 nm2 at 0 and 20
mN/m surface tension respectively using same mdp file and other conditions
as mentioned above for only 1024 DPPC lipids. This result correlates with
the experimental results.
Sincerely Your’s
Sheikh Imamul Hossain
PhD Student at QUT